use rusage to make sure there is enough disk space. lsrcp now uses ecs2c as...

use rusage to make sure there is enough disk space. lsrcp now uses ecs2c as the host machine for coping etc to protect NFS. Make sure number of jobs is greater than 1 else arrays dont like it

misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm

@@ -102,8 +102,20 @@ sub submit_exonerate {
   my $queryfile = basename($query);
   my $targetfile = basename($target);
 
+  my $disk_space_needed = (stat($query))[7]+(stat($target))[7];
+
+  $disk_space_needed /= 1024000; # convert to MB
+  $disk_space_needed = int($disk_space_needed);
+  $disk_space_needed += 1;
+#  print "disk space needed = ".$disk_space_needed."\n";
+
   my $num_jobs = calculate_num_jobs($query);
 
+  # array features barf if just one job 
+  if($num_jobs == 1){
+    $num_jobs++;
+  }
+
   $self->jobcount($self->jobcount()+$num_jobs);
 
   my $options_str = join(" ", @options);
@@ -117,9 +129,11 @@ sub submit_exonerate {
 
   my $output = $self->get_class_name() . "_" . $ensembl_type . "_" . "\$LSB_JOBINDEX.map";
 
-  my @main_bsub = ( 'bsub', '-J' . $unique_name . "[1-$num_jobs]", '-o', "$prefix.%J-%I.out", '-e', "$prefix.%J-%I.err");
+  my @main_bsub = ( 'bsub', '-R' .'rusage[tmp='.$disk_space_needed.']',  '-J' . $unique_name . "[1-$num_jobs]", '-o', "$prefix.%J-%I.out", '-e', "$prefix.%J-%I.err");
+
+#  my @main_bsub = ( 'bsub', '-J' . $unique_name . "[1-$num_jobs]", '-o', "$prefix.%J-%I.out", '-e', "$prefix.%J-%I.err");
 
-  #print "bsub command: " . join(" ", @main_bsub) . "\n\n";
+#  print "bsub command: " . join(" ", @main_bsub) . "\n\n";
 
   # Create actual execute script to be executed with LSF, and write to pipe
   my $main_job = <<EOF;
@@ -129,12 +143,12 @@ cd /tmp
 
 rm -f /tmp/\$LSB_JOBINDEX.$queryfile /tmp/\$LSB_JOBINDEX.$targetfile /tmp/$output
 
-lsrcp $target /tmp/\$LSB_JOBINDEX.$targetfile
-lsrcp $query  /tmp/\$LSB_JOBINDEX.$queryfile
+lsrcp ecs2c:$target /tmp/\$LSB_JOBINDEX.$targetfile
+lsrcp ecs2c:$query  /tmp/\$LSB_JOBINDEX.$queryfile
 
 $exonerate_path /tmp/\$LSB_JOBINDEX.$queryfile /tmp/\$LSB_JOBINDEX.$targetfile --querychunkid \$LSB_JOBINDEX --querychunktotal $num_jobs --showvulgar false --showalignment FALSE --ryo "xref:%qi:%ti:%ei:%ql:%tl:%qab:%qae:%tab:%tae:%C:%s\n" $options_str | grep '^xref' > /tmp/$output
 
-lsrcp /tmp/$output $root_dir/$output
+lsrcp /tmp/$output ecs2c:$root_dir/$output
 
 rm -f /tmp/\$LSB_JOBINDEX.$queryfile /tmp/\$LSB_JOBINDEX.$targetfile /tmp/$output
 EOF